Uses of Class
net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE

Packages that use SiteScore.SITE_SCORE_TYPE

Package	Description
net.maizegenetics.dna.snp	Data structures for holding SNP and indel variation across taxa (samples) and genomic positions.
net.maizegenetics.dna.snp.byte2d
net.maizegenetics.dna.snp.score	Support for site scores (for example quality scores or imputation accuracy).
net.maizegenetics.phenotype	Phenotype (future) and Trait (deprecated) currently both define classes for holding trait data.

Uses of SiteScore.SITE_SCORE_TYPE in net.maizegenetics.dna.snp

Methods in net.maizegenetics.dna.snp that return types with arguments of type SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
Set<SiteScore.SITE_SCORE_TYPE>	CombineGenotypeTable.siteScoreTypes()
Set<SiteScore.SITE_SCORE_TYPE>	CoreGenotypeTable.siteScoreTypes()
Set<SiteScore.SITE_SCORE_TYPE>	GenotypeTable.siteScoreTypes() Return the site scores types that have value for this genotype table.
Set<SiteScore.SITE_SCORE_TYPE>	MergedGenotypeTable.siteScoreTypes()
Set<SiteScore.SITE_SCORE_TYPE>	TOPMGenotypeTable.siteScoreTypes()

Methods in net.maizegenetics.dna.snp with parameters of type SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
float	CombineGenotypeTable.alleleProbability(int taxon, int site, SiteScore.SITE_SCORE_TYPE type)
float	CoreGenotypeTable.alleleProbability(int taxon, int site, SiteScore.SITE_SCORE_TYPE type)
float	GenotypeTable.alleleProbability(int taxon, int site, SiteScore.SITE_SCORE_TYPE type)
float	MergedGenotypeTable.alleleProbability(int taxon, int site, SiteScore.SITE_SCORE_TYPE type)
float	TOPMGenotypeTable.alleleProbability(int taxon, int site, SiteScore.SITE_SCORE_TYPE type)

Uses of SiteScore.SITE_SCORE_TYPE in net.maizegenetics.dna.snp.byte2d

Methods in net.maizegenetics.dna.snp.byte2d that return SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
SiteScore.SITE_SCORE_TYPE	AbstractByte2D.siteScoreType()
SiteScore.SITE_SCORE_TYPE	Byte2D.siteScoreType()

Methods in net.maizegenetics.dna.snp.byte2d with parameters of type SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
static Byte2D	Byte2DBuilder.getInstance(ch.systemsx.cisd.hdf5.IHDF5Reader reader, SiteScore.SITE_SCORE_TYPE siteScoreType)
static Byte2DBuilder	Byte2DBuilder.getInstance(ch.systemsx.cisd.hdf5.IHDF5Writer writer, int numSites, SiteScore.SITE_SCORE_TYPE siteScoreType, TaxaList taxaList)
static Byte2DBuilder	Byte2DBuilder.getInstance(int numTaxa, int numSites, SiteScore.SITE_SCORE_TYPE siteScoreType, TaxaList taxaList)

Constructors in net.maizegenetics.dna.snp.byte2d with parameters of type SiteScore.SITE_SCORE_TYPE

Constructor and Description
AbstractByte2D(SiteScore.SITE_SCORE_TYPE scoreType, int numTaxa, int numSites)

Uses of SiteScore.SITE_SCORE_TYPE in net.maizegenetics.dna.snp.score

Fields in net.maizegenetics.dna.snp.score declared as SiteScore.SITE_SCORE_TYPE

Modifier and Type	Field and Description
static SiteScore.SITE_SCORE_TYPE[]	AlleleDepth.ALLELE_DEPTH_TYPES
static SiteScore.SITE_SCORE_TYPE[]	AlleleProbability.ALLELE_PROBABILITY_TYPES

Methods in net.maizegenetics.dna.snp.score that return SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
static SiteScore.SITE_SCORE_TYPE	SiteScore.SITE_SCORE_TYPE.valueOf(String name) Returns the enum constant of this type with the specified name.
static SiteScore.SITE_SCORE_TYPE[]	SiteScore.SITE_SCORE_TYPE.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in net.maizegenetics.dna.snp.score that return types with arguments of type SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
Set<SiteScore.SITE_SCORE_TYPE>	AlleleDepth.siteScoreTypes()
Set<SiteScore.SITE_SCORE_TYPE>	AlleleProbability.siteScoreTypes()
Set<SiteScore.SITE_SCORE_TYPE>	Dosage.siteScoreTypes()
Set<SiteScore.SITE_SCORE_TYPE>	ReferenceProbability.siteScoreTypes()
Set<SiteScore.SITE_SCORE_TYPE>	SiteScore.siteScoreTypes() Return the site scores types.

Methods in net.maizegenetics.dna.snp.score with parameters of type SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
AlleleProbabilityBuilder	AlleleProbabilityBuilder.addTaxon(int taxon, byte[] values, SiteScore.SITE_SCORE_TYPE type)
AlleleProbabilityBuilder	AlleleProbabilityBuilder.addTaxon(int taxon, float[] values, SiteScore.SITE_SCORE_TYPE type)
AlleleDepthBuilder	AlleleDepthBuilder.addTaxon(int taxon, int[] values, SiteScore.SITE_SCORE_TYPE type)
int	AlleleDepth.value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth of nucleotide (scoreType) at given taxon and site.
float	AlleleProbability.value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType)
int	FilterAlleleDepth.value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth of nucleotide (scoreType) at given taxon and site.
float	FilterAlleleProbability.value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType)
int	HDF5AlleleDepth.value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth of nucleotide (scoreType) at given taxon and site.
int	MaskAlleleDepth.value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType)
float	MaskAlleleProbability.value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType)
byte	AlleleDepth.valueByte(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth (byte representation) of nucleotide (scoreType) at given taxon and site.
byte	FilterAlleleDepth.valueByte(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth (byte representation) of nucleotide (scoreType) at given taxon and site.
byte	FilterHDF5AlleleDepth.valueByte(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth (byte representation) of nucleotide (scoreType) at given taxon and site.
byte	HDF5AlleleDepth.valueByte(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth (byte representation) of nucleotide (scoreType) at given taxon and site.
byte	MaskAlleleDepth.valueByte(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType)

Uses of SiteScore.SITE_SCORE_TYPE in net.maizegenetics.phenotype

Methods in net.maizegenetics.phenotype with parameters of type SiteScore.SITE_SCORE_TYPE

Modifier and Type	Method and Description
float[]	GenotypePhenotype.alleleProbsOfType(SiteScore.SITE_SCORE_TYPE type, int site)